You can put your OS and programs on one drive and use the second hard drive for storage, basically how my systems are set up. The drive with the OS and programs would be the Master and the storage drive would be the Slave. There are no Master or Slave with SATA drives. Currently the drive I use for OS and programs is an ATA drive and my storage drives are SATA. In this case, the ATA drive is set up as though it's the only drive, i.e., the 3rd setting the other 2 being Slave or Master.